git://source.jalview.org / jalview.git / commitdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | patch | inline | side by side (parent: 412f54e)
JAL-1788 added help documentation for biojson
authortcofoegbu <tcnofoegbu@dundee.ac.uk>
Mon, 13 Jul 2015 16:41:47 +0000 (17:41 +0100)
committertcofoegbu <tcnofoegbu@dundee.ac.uk>
Mon, 13 Jul 2015 16:41:47 +0000 (17:41 +0100)
help/html/features/bioJsonFormat.html [new file with mode: 0644] patch | blob
help/html/features/clarguments.html patch | blob | history
help/html/io/fileformats.html patch | blob | history
help/html/menus/alignmentMenu.html patch | blob | history
src/jalview/bin/Jalview.java patch | blob | history

diff --git a/help/html/features/bioJsonFormat.html b/help/html/features/bioJsonFormat.html
new file mode 100644 (file)
index 0000000..341e3e2
--- /dev/null
+++ b/help/html/features/bioJsonFormat.html
@@ -0,0 +1,52 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>BioJson-1.0 A JSON File Format</title>
+</head>
+<body>
+       <h1>BioJson (version-1.0)</h1>
+       BioJson is a standardise JavaScript Object Notation (JSON) format for exchange of Bio-informatics Sequence Alignment data.      
+       BioJSon-1.0 schema/documentation is available <a href="http://www.jalview.org/builds/develop/examples/biojson-doc/">here</a>.
+       You can keep up to date with BioJson development and latest news <a href="https://github.com/jalview/biojson/wiki">here</a>.
+       
+       <h2>Features supported</h2>
+       Export/Import of the following alignment elements are supported in BioJson-1.0:
+       <ul>
+               <li>Alignment Sequences</li>
+               <li>Alignment Features</li>
+               <li>Alignment Annotations</li>
+               <li>Sequence Groups</li>
+               <li>Color Scheme</li>
+               <li>Hidden Sequences</li>
+               <li>Hidden Columns</li>
+       </ul>
+
+       <h2>Features not yet supported</h2>
+       Export/Import of the following alignment elements are not supported in BioJson-1.0:
+       <ul>
+               <li>Reference sequence</li>
+               <li>Representative sequence</li>
+               <li>Trees</li>
+               <li>3D Structures</li>
+       </ul>
+</body>
+</html>
diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 8a72d4d..16b0dc0 100644 (file)
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -182,6 +182,10 @@
  <td><div align="center">-blc FILE</div></td>
  <td><div align="left">Create alignment file FILE in BLC format.</div></td>
  </tr>
+  <tr> 
+ <td><div align="center">-json FILE</div></td>
+ <td><div align="left">Create alignment file FILE in JSON format.</div></td>
+ </tr>
  <tr> 
  <td><div align="center">-jalview FILE</div></td>
 
diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index ae56945..b457adf 100755 (executable)
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -77,6 +77,11 @@ THISISASEQUENCE<br></td>
 <em>...</em><br>//</td>
 <td width="23%">.phy</td>
 </tr>
+<tr>
+<td width="17%">JSON</td>
+<td width="60%">Data starts with '{' <br>Data  ends with '}' <br><br>See <a href="../features/bioJsonFormat.html">BioJson</a> for more info about Jalview JSON format <br></td>
+<td width="23%">.json</td>
+</tr>
 </table>
 <p>The file extensions are used to associate jalview alignment icons
 with alignment files: <img src="file.png" width=12 height=12 >
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index a2cb603..8b50d9e 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -72,6 +72,7 @@
                                                <li><strong>AMSA</strong></li>
                                                <li><strong>STH</strong></li>
                                                <li><strong>Phylip</strong></li>
+                                               <li><strong>JSON</strong></li>
                                        </ul></li>
                                <li><strong>Print (Control P)<br> </strong><em>Jalview
                                                will print the alignment using the current fonts and colours of
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8ad4cbd..177d56f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -693,6 +693,7 @@ public class Jalview
                     + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
                     + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
                     + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
                     + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"